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CGATOxford / UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets
MIT License
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Conda issue: IndexError: list index out of range #536

Closed CWYuan08 closed 2 years ago

CWYuan08 commented 2 years ago

Hi, umi_tools has always been working for me, but suddenly when I tried to put together a pipeline, it came to this error, for any command I use after umi_tools, (e.g. umi_tools dedup..):

Traceback (most recent call last): File "/miniconda3/envs/umitools/bin/umi_tools", line 8, in sys.exit(main()) File "/miniconda3/envs/umitools/lib/python3.7/site-packages/umi_tools/umi_tools.py", line 53, in main elif argv[2] in ["--help", "-h", "--help-extended"]: IndexError: list index out of range

However, when I just type umi_tools, there isn't any error.

Do you know how I could resolve this?

Thank you very much!

CWYuan08 commented 2 years ago

Hi @IanSudbery, sorry to bother again, I'm still getting the same issue, what should I do to resolve this..? Thank you very much!

Best, CW

IanSudbery commented 2 years ago

Hi,

You are getting this error because you are executing umi_tools dedup etc, without any other options, and dedup etc requirement than just the name of the tool. We have edited the code so that the help should be output in this situation (if you pull the latest version of the master branch), but even with the last released version, you can avoid this by typing umi_tools dedup --help in order to get the help.

CWYuan08 commented 2 years ago

Dear @IanSudbery,

thank you. I see, it worked!

Best regards, CW